Jürgen Klopp has long been touted as a future Bundestrainer, and on Saturday, the 45-year-old proved that he's totally up to the job: he sprang a 3-5-2 formation on his unsuspecting team a few minutes before kick-off, exactly like Jogi Löw had done in the 3-3 friendly in the Ukraine a year ago.

Unfortunately the consequences of this brain wave – or brain freeze? – were even worse than those endured by the national team. Dortmund were so befuddled by playing with Mats Hummels, Sven Bender and Neven Subotic at the back in the Ruhr derby that Schalke simply had to turn up and look vaguely competent to dominate proceedings. Klopp changed it back to a 4-2-3-1 after 29 minutes but by then the Royal Blues were already 1-0 up thanks to a fine Ibrahim Afellay strike. The champions never quite found their stride again. "I wanted to help the team," Klopp said later, full of contrition.

On paper, it might have made sense. Shorn of Jakub "Kuba" Blaszczykowski on the right and Marcel Schmelzer on the left, Dortmund were incomplete on both flanks, so the idea to make do without inadequate replacements and to adopt a wing-back system had some logic. But the 23-year-old Bender has never played as a sweeper before – he probably had to look up "libero" in the Fremdwörterduden (loanwords dictionary) – and a bit of practice beforehand probably wouldn't have gone amiss either.

More changes followed. Kevin Grosskreutz, who had started as the left-back, moved into four (some say five) different positions during the course of the game. Schalke, after Marco Höger had doubled the lead with a fine counter-attack, kept their cool in spite of a belated reaction from the hosts. The hosts finally got going, to an extent, when Robert Lewandowski made it 2-1 with 35 minutes left.

Schalke stood firm, though. Late disappointments against Montpellier (1-1) and Düsseldorf (2-2) have taught Huub Stevens' team the importance of seeing out games. They cleverly played for time, too: the keeper Lars Unnerstall used a barrage of missiles from the stands to his advantage and took forever to take his goal-kick. "If anyone needs a lighter, there are lots of them in the goal," said the goalie, who was eventually booked for time-wasting. "I don't smoke, I don't need them really. I was also hit by a 20 cent coin".

Hummels angrily remarked that he had never seen "such a fair team" as the local rivals but then tried to down-play the significance of the result later on. "It's irrelevant that we have lost, and it would have been irrelevant if we had won, too," claimed the Germany centre-back. That's not how it felt on the day, however. For Schalke, their first derby win in three years was confirmation that they are Bayern's likeliest challengers for the title this season and – for now – a better team than their neighbours.

"I think I might have a glass of wine tonight," said Stevens, with the merest hint of a satisfied smile. His men will visit the Emirates with a renewed sense of confidence and the knowledge that their excellent organisation could well frustrate Arsenal on Wednesday night.

Dortmund also learnt a lot about themselves. It wasn't just a combination of the unfamiliar system and a strange lack of energy that did for them ("nothing to do with the formation, we simply played badly," said Marco Reus). The lack of depth in the squad was also apparent. Borussia have certainly strengthened by contrast with last season but are still not in a position where they can replace four key players like Ilkay Gündogan, Schmelzer, "Kuba" and Mario Götze. The demanding match schedule is taking its toll this autumn and a 12-point gap behind leaders Bayern will be very difficult to make up.

The good news is that Gündogan, Schmelzer and Götze should be back for Wednesday night's enticing visit of Real Madrid. Dortmund will surely show a strong reaction; if anything, the disappointment in the league will make them even more determined to succeed in the Champions League this season. The refusal of the manager and the players to blame each other for the painful Schalke defeat also points to a strong togetherness in the camp. "We didn't play well and I have to take responsibility for that," said Klopp with an honesty that contrasts markedly with Löw's stubborn post-Italy denials. Maybe he's not quite ready for the Germany job yet, after all.

Talking Points

• The derby sadly made headlines for all the wrong reasons as well. One hundred and eighty troublemakers from both sides were arrested after fighting in the city centre and attacking police officers with cobblestones and bottles. "It was a declaration of war on the police," said Arnold Plickert, the head of the police officers' union in North Rhine-Westphalia. This was, apparently, not a spontaneous riot but a largely organised ruckus. Matchday bans and stronger sanctions were needed, Plickert argued, and it's difficult not to agree after the worst incident of hooliganism in the city since the 2006 World Cup. "The enemies of football need punishing, we can't allow them to ruin if for the vast majority of fans," demanded the local paper Westdeutsche Allgemeine Zeitung in an editorial. Inside the ground it had been largely peaceful, incidentally, bar some attempts by Dortmund supporters to take the Schalke end when the visiting fans were goading them with a stolen banner.

• Bayern Munich had one really difficult moment to endure in Düsseldorf: going 4-0 up after Thomas Müller's second goal brought back all the horrible memories of the 4-4 draw with Sweden for the seven Germany internationals on the pitch. Thankfully, the substitute Rafinha made sure that the doubts couldn't linger for long. The Brazilian added a fifth with three minutes to go. It was Bayern's eighth win in eight, a new record in the Bundesliga. And away from the numbers, it was pretty impressive stuff, too: they pressed and pressed against the hapless Fortuna until Norbert Meier's side resembled a sad, wrinkled pair of empty lemon skins. Sandwiched between an international week and a tricky Champions League match away to Lille on Tuesday, this was the kind of appointment that could have ended with a lacklustre draw or worse. But Fortuna were unlucky – pardon the pun – to come up against players who were keen to make up for the embarrassment against Sweden and push home their advantage with relentless application.

Franck Ribéry was also really in the mood following a rare convincing outing for France and the return of the left-back David Alaba bodes very well for the future. "Nothing is decided," said Karl-Heinz Rummenigge. But Bayern's consistency and tremendous depth certainly looks ominous. "The league capitulates!" declared Bild.

• Wolfsburg also look as if they don't quite belong in the Bundesliga, albeit for very different reasons. The crowd in the Volkswagen-Arena were singing "Oh what a beautiful day" in an ironic manner when they saw their side slump to yet another defeat to SC Freiburg. They're bottom of the table now, miles away from qualifying for a European place. That's good news in the sense that Uefa will not be forced to examine their complex and rather murky system of corporate subsidies and sub-contractor sponsors – Kuka, a producer of car manufacturing robots, advertise in the stadium, among others – but bad news for the coach, general manager and sporting director, Felix Magath, who will have to give serious thought to firing himself. The 59-year-old has already gone through more captains in this campaign than your average siren and, from one day to the next, no player can be quite sure if he's a key player, a regular, on the bench, with the reserves or due to be transferred to Moldova.

Nothing do to with Magath, of course. "We were already unsettled before," he said after the 2-0 capitulation. Well-placed sources think Volkswagen will give him two more games before they'll attempt to emulate the recent stunt of another free-falling Felix – with a reverse trajectory.